IL_8RJD_119

3D structure

PDB id

8RJD (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2

Experimental method

ELECTRON MICROSCOPY

Resolution

2.78574 Å

Loop

Sequence

GAA*UACC

Length

7 nucleotides

Bulged bases

8RJD|1|K|A|3901, 8RJD|1|K|C|4560

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

IL_8RJD_119 not in the Motif Atlas

Homologous match to IL_5TBW_092

Geometric discrepancy: 0.0849

The information below is about IL_5TBW_092

Detailed Annotation

Major groove platform with intercalation

Broad Annotation

Major groove platform

Motif group

IL_54678.7

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

5

Unit IDs

8RJD|1|K|G|3900
8RJD|1|K|A|3901
8RJD|1|K|A|3902
*
8RJD|1|K|U|4558
8RJD|1|K|A|4559
8RJD|1|K|C|4560
8RJD|1|K|C|4561

Current chains

Chain K

28S rRNA

Nearby chains

Chain B

Nascent chain

Chain P

uL22

Chain w

Ribosomal protein L3